Resource
| Id | DNase-seq/ENCSR000ELY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000ELY [biosample_summary="Homo sapiens AG04450"] |
| Description |
status: released biological_replicates: Rep 2 summary: output_type: peaks audit_warning: Alignment file {ENCFF088CFN|/files/ENCFF088CFN/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 22224225 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) audit_warning: Alignment file {ENCFF761RMZ|/files/ENCFF761RMZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 28443646 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) audit_warning: Signal Portion of Tags (SPOT) is a measure of enrichment, analogous to the commonly used fraction of reads in peaks metric. ENCODE processed alignment files {ENCFF761RMZ|/files/ENCFF761RMZ/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.39. According to ENCODE standards, SPOT1 score of 0.4 or higher is considered a product of high quality data. Any sample with a SPOT1 score <0.3 should be targeted for replacement with a higher quality sample, and a SPOT1 score of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000ELY | float |
DNase-seq_ENCSR000ELY |
DNase-seq ENCSR000ELY [biosample_summary="Homo sapiens AG04450"]
|
 |
[0.248, 35.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 11755697 | 0.37% | 66900 |
| chr1 | 1113517 | 0.45% | 6357 |
| chr2 | 991549 | 0.41% | 5642 |
| chr3 | 789000 | 0.40% | 4481 |
| chr4 | 597667 | 0.31% | 3459 |
| chr5 | 661710 | 0.36% | 3783 |
| chr6 | 734148 | 0.43% | 4192 |
| chr7 | 580193 | 0.36% | 3303 |
| chr8 | 548304 | 0.38% | 3172 |
| chr9 | 487796 | 0.35% | 2779 |
| chr10 | 556601 | 0.42% | 3199 |
| chr11 | 613842 | 0.45% | 3461 |
| chr12 | 580163 | 0.44% | 3283 |
| chr13 | 322655 | 0.28% | 1860 |
| chr14 | 358336 | 0.33% | 2044 |
| chr15 | 394075 | 0.39% | 2252 |
| chr16 | 380477 | 0.42% | 2148 |
| chr17 | 496458 | 0.60% | 2772 |
| chr18 | 253385 | 0.32% | 1471 |
| chr19 | 405670 | 0.69% | 2173 |
| chr20 | 274043 | 0.43% | 1543 |
| chr21 | 138420 | 0.30% | 783 |
| chr22 | 208313 | 0.41% | 1183 |
| chrX | 260082 | 0.17% | 1501 |
| chrY | 9293 | 0.02% | 59 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 66900 | 2 | 700 | 175.72 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF816RDX.bed.gz | 709.9 KB | 65cc8f4c23460163ac548597e1a44022 |
| ENCFF816RDX.tabix.bed.gz | 631.09 KB | 4b5c768e46e0bdabe3bd9304492d92ad |
| ENCFF816RDX.tabix.bed.gz.tbi | 360.75 KB | aa16cce29aa1029385ce1c1b4eb39d8c |
| genomic_resource.yaml | 3.2 KB | e4adc46a3e3d0148c939d11f370cab12 |
| statistics/ |